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Dr. Fabian Müller

Dr. Fabian Müller

Max-Planck-Institut für Informatik
Research Group Computational Biology

Campus E1 4
66123 Saarbrücken, Germany
email:   muellerf@stanford.edu
phone:   +49 681 9325 3009
fax:   +49 681 9325 3099
room:   509 (Building E1 4)

Publications

  1. Amabile*, G., Di Ruscio*, A., Müller*, F., Welner, R. S., Yang, H., Ebralidze, A. K., Zhang, H., Levantini, E., Qi, L., Martinelli, G., Brummelkamp, T., Le Beau, M. M., Figueroa, M. E., Bock, C., Tenen, D. G.
    Dissecting the role of aberrant DNA methylation in human leukaemia
    Nature Communications, 6, 7091, 2015, http://doi.org/10.1038/ncomms8091
    (Abstract)

  2. Assenov*, Y., Müller*, F., Lutsik*, P., Walter, J., Lengauer, T., Bock, C.
    Comprehensive Analysis of DNA Methylation Data with RnBeads.
    Nature Methods, 11(11), 1138–1140, 2014, doi:10.1038/nmeth.3115
    (Abstract)

  3. Farlik, M., Halbritter, F., Müller*, F., Choudry, F. A., Ebert, P., Klughammer, J., Farrow, S., Santoro, A., Ciaurro, V., Mathur, A., Uppal, R., Stunnenberg, H. G., Ouwehand, W. H., Laurenti, E., Lengauer, T., Frontini, M., Bock, C.
    DNA Methylation Dynamics of Human Hematopoietic Stem Cell Differentiation.
    Cell Stem Cell, 19, 2016, doi:10.1016/j.stem.2016.10.019
    (Abstract)

  4. Ziller*, M. J., Müller*, F., Liao, J., Zhang, Y., Gu, H., Bock, C., Boyle, P., Epstein C. B., Bernstein, B. E., Lengauer, T., Gnirke, A., Meissner, A.
    Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types
    PLoS Genetics, 7(12), 2011, e1002389. doi:10.1371/journal.pgen.1002389.t001
    (Abstract)

  5. Ziller, M. J., Gu, H., Müller, F., Donaghey, J., Tsai, L. T. Y., Kohlbacher, O., De Jager, P. E., Rosen, E. D., Bennett, D. A., Bernstein, B. E., Gnirke, A., Meissner, A.
    Charting a dynamic DNA methylation landscape of the human genome.
    Nature, 500(7463):477-81, 2013, doi:10.1038/nature12433
    (Abstract)

  6. Durek, P., Nordström, K., Gasparoni, G., Salhab, A., Kressler, C., de Almeida, M., et al.
    Epigenomic Profiling of Human CD4+ T Cells Supports a Linear Differentiation Model and Highlights Molecular Regulators of Memory Development
    Immunity, 45(5), 2016, doi:10.1016/j.immuni.2016.10.022
    (Abstract)

  7. Wallner, S., Schröder, C., Leitão, E., Berulava, T., Haak, C., Beisser, D., et al.
    Epigenetic dynamics of monocyte-to-macrophage differentiation
    Epigenetics & Chromatin, 9(1), 2016, doi:10.1186/s13072-016-0079-z
    (Abstract)

  8. Ebert, P., Müller, F., Nordström, K., Lengauer, T., Schulz, M. H.
    A general concept for consistent documentation of computational analyses
    Database, 2015, doi:10.1093/database/bav050
    (Abstract)

  9. Martínez-Cardús, A., Moran, S., Musulen, E., Moutinho, C., Manzano, J. L., Martinez-Balibrea, E., Tierno, M., Élez, E., Landolfi, S., Lorden, P., Arribas, C., Müller, F., Bock, C., Taberno, J., Esteller, M.
    Epigenetic Homogeneity Within Colorectal Tumors Predicts Shorter Relapse-free and Overall Survival Times for Patients With Loco-regional Cancer
    Gastroenterology, 2016, doi:10.1053/j.gastro.2016.08.001
    (Abstract)

  10. Planello, A. C., Ji, J., Sharma, V., Singhania, R., Mbabaali, F., Müller, F., Alfaro, J. A., Bock, C., De Carvalho, D. D., Batada, N. N.
    Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors
    Cell Regeneration, 3(1), 4, 2014, doi:10.1186/2045-9769-3-4
    (Abstract)

  11. Sandoval, J., Mendez-Gonzalez, J., Nadal, E., Chen, G., Carmona, F. J., Sayols, S., Moran, S., Heyn, H., Vizoso, M., Gomez, A., Sanchez-Cespedes, M., Assenov, Y., Müller, F., Bock, C., Taron, M., Mora, J., Muscarella, L.A., Liloglou, T., Davies, M., Pollan, M., Pajares, M.J., Torre, W., Montuenga, L.M., Brambilla, E., Field, J.K., Roz, L., Lo Iacono, M., Scagliotti, G.V., Rosell, R., Beer, D.G., Esteller, M.
    A Prognostic DNA Methylation Signature for Stage I Non-Small-Cell Lung Cancer
    Journal of Clinical Oncology, 2013, doi:10.1200/JCO.2012.48.5516
    (Abstract)

  12. Deplus, R., Blanchon, L., Rajavelu, A., Boukaba, A., Defrance, M., Luciani, J., Rothé, F., Dedeurwaerder, S., Denis, H., Brinkman, A. B., Simmer, F., Müller, F., Bertin, B., Berdasco, M., Putmans, P., Calonne, E., Litchfield, D. W., de Launoit, Y., Jurkowski, T., Stunnenberg, H. G., Bock, C., Sotiriou, C., Fraga, M. F., Esteller, M., Jeltsch, A., Fuks, F.
    Regulation of DNA methylation patterns by CK2-mediated phosphorylation of Dnmt3a
    CellReports, 8(3):743–753, 2014, doi:10.1016/j.celrep.2014.06.048
    (Abstract)

  13. Tobi, E. W., Goeman, J. J., Monajemi, R., Gu, H., Putter, H., Zhang, Y., Slieker, R. C., Stok, A. P., Thijssen, P. E., Müller, F., van Zwet, E. W., Bock, C., Meissner, A., Lumey, L. H., Slagboom, P. E., Heijmans, B. T.
    DNA methylation signatures link prenatal famine exposure to growth and metabolism
    Nature Communications, 5:5592, 2014, doi:10.1038/ncomms6592
    (Abstract)

  14. Schneider, E., Hajj, El, N., Müller, F., Navarro, B., & Haaf, T.
    Epigenetic Dysregulation in the Prefrontal Cortex of Suicide Completers
    Cytogenetic and Genome Research, 2015, doi:10.1159/000435778
    (Abstract)

  15. Xi, Y., Bock, C., Müller, F., Sun, D., Meissner, A., Li, W.
    RRBSMAP: A Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing
    Bioinformatics, 2011 doi: 10.1093/bioinformatics/btr668
    (Abstract)

  16. Bock, C., Tomazou, E., Brinkman, A., Müller, F., Simmer, F., Gu, H., Jäger, N., Gnirke, A., Stunnenberg, H., Meissner, A.
    Quantitative comparison of genome-wide DNA methylation mapping technologies
    Nature Biotechnology, 28(10):1106-1114, 2010.
    (Abstract)

  17. Feuerbach, L., Halachev, K., Assenov, Y., Müller, F., Bock, C., Lengauer, T.
    Analyzing epigenome data in context of genome evolution and human diseases
    Evolutionary Genomics, Methods in molecular biology, 856, 431-467. doi:10.1007/978-1-61779-585-5_18, 2012.
    (Abstract)

  18. Saigo, H., Altmann, A., Bogojeska, J., Müller, F., Nowozin, S., Lengauer, T.
    Learning from Past Treatments and Their Outcome Improves Prediction of In Vivo Response to Anti-HIV Therapy
    Statistical Applications in Genetics and Molecular Biology, 10(1), 2011.
    (Abstract)

  19. Müller, F.
    Analyzing DNA Methylation Signatures of Cell Identity
    PhD Thesis, doi:10.17617/2.2474737, 2017.
    (Abstract)

  20. Müller, F.
    Assessing Antibody Neutralization of HIV-1 as an Initial Step in the Search for gp160-based Immunogens
    Master's Thesis, 2009.
    (Thesis (PDF))

  21. Müller, F.
    Inferring virological response to antiretroviral combination therapy based on past treatment lines
    Bachelor's Thesis, 2008.
    (Thesis (PDF))